Genome-wide expression profiling in Geobacter sulfurreducens: identification of Fur and RpoS transcription regulatory sites in a rel_Gsu mutant

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• 作者：Julia Krushkal ; Bin Yan ; Laurie N. DiDonato ; Marko Puljic ; Kelly P. Nevin ; Trevor L. Woodard ; Ronald M. Adkins ; Barbara A. Meth¨¦ and Derek R. Lovley
• 关键词：Guanosine 3′ ; 5′ ; bispyrophosphate ; ppGpp ; RelA ; Promoter
• 刊名：Functional & Integrative Genomics
• 出版年：2007
• 出版时间：July, 2007
• 年：2007
• 卷：7
• 期：3
• 页码：229-255
• 全文大小：466 KB

文摘

Rel_Gsu is the single Geobacter sulfurreducens homolog of RelA and SpoT proteins found in many organisms. These proteins are involved in the regulation of levels of guanosine 3′, 5′ bispyrophosphate, ppGpp, a molecule that signals slow growth and stress response under nutrient limitation in bacteria. We used information obtained from genome-wide expression profiling of the rel _Gsu deletion mutant to identify putative regulatory sites involved in transcription networks modulated by Rel_Gsu or ppGpp. Differential gene expression in the rel _Gsu deletion mutant, as compared to the wild type, was available from two growth conditions, steady state chemostat cultures and stationary phase batch cultures. Hierarchical clustering analysis of these two datasets identified several groups of operons that are likely co-regulated. Using a search for conserved motifs in the upstream regions of these co-regulated operons, we identified sequences similar to Fur- and RpoS-regulated sites. These findings suggest that Fur- and RpoS-dependent gene expression in G. sulfurreducens is affected by Rel_Gsu-mediated signaling.